fp <-here('vast','output','opilio_gadus_numbers')
setwd(fp)
load(paste0(fp,"/Record.RData"))
list2env(Record,envir = environment())
## <environment: R_GlobalEnv>
Record
## $Version
## [1] "VAST_v8_0_0"
##
## $Method
## [1] "Mesh"
##
## $n_x
## [1] 50
##
## $Aniso
## [1] 1
##
## $FieldConfig
## Omega1 Epsilon1 Omega2 Epsilon2
## 5 5 5 5
##
## $RhoConfig
## Beta1 Beta2 Epsilon1 Epsilon2
## 0 0 0 0
##
## $OverdispersionConfig
## Eta1 Eta2
## 0 0
##
## $VamConfig
## Method Rank Timing
## 0 0 0
##
## $ObsModel
## [1] 1 0
##
## $Region
## [1] "Eastern_Bering_Sea"
##
## $Species_set
## [1] "Opilio immature" "Opilio spawner" "small cod" "medium cod"
## [5] "large cod"
##
## $strata.limits
## STRATA
## 1 All_areas
##
## $Options
## SD_site_density SD_site_logdensity Calculate_Range
## 0 0 1
## Calculate_evenness Calculate_effective_area Calculate_Cov_SE
## 0 1 0
## Calculate_Synchrony Calculate_Coherence
## 0 0
Catch rate
knitr::include_graphics(paste0(fp,"/maps--catchrate_pearson_resid.png"))
Encounter rate
knitr::include_graphics(paste0(fp,"/Diag--Encounter_prob.png"))
knitr::include_graphics(paste0(fp,"/maps--encounter_pearson_resid.png"))
knitr::include_graphics(paste0(fp,"/Aniso.png"))
# Opilio immature
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-1.jpg"))
# Spawners
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-2.jpg"))
# Small cod
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-3.jpg"))
# Medium cod
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-4.jpg"))
# Large cod
knitr::include_graphics(paste0(fp,"/QQ_Fn/Posterior_Predictive-Histogram-5.jpg"))
Columnns: Omega, Epsilon (Spatial, Temporal variation, respectively)
Rows: Encounter probability, Positive catch rate
knitr::include_graphics(paste0(fp,"/Cov--Analytic.png"))
knitr::include_graphics(paste0(fp,"/Index-Biomass.png"))
knitr::include_graphics(paste0(fp,"/center_of_gravity.png"))
knitr::include_graphics(paste0(fp,"/Effective_Area.png"))
knitr::include_graphics(paste0(fp,"/dens_Opilio Immature.png"))
knitr::include_graphics(paste0(fp,"/dens_Opilio Spawner.png"))
knitr::include_graphics(paste0(fp,"/dens_Small Cod.png"))
knitr::include_graphics(paste0(fp,"/dens_Medium Cod.png"))
knitr::include_graphics(paste0(fp,"/dens_Large Cod.png"))
knitr::include_graphics(paste0(fp,"/spp_correlations.png"))
knitr::include_graphics(paste0(fp,"/factor_loadings_rotated.png"))
# Omega 1 (encounter probability, spatial variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Omega1.png"))
# Omega 2 (positive catch rate, spatial variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Omega2.png"))
# Epsilon 1 (encounter probability, spatiotemporal variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Epsilon1.png"))
# Epsilon 2 (positive catch rate, spatiotemporal variation)
knitr::include_graphics(paste0(fp,"/Factor_maps--Epsilon2.png"))
# Factor 1, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_1.png"))
# Factor 2, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_2.png"))
# Factor 3, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_3.png"))
# Factor 4, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_4.png"))
# Factor 5, Positive Catch Rate
knitr::include_graphics(paste0(fp,"/Eps_Pos--Factor_5.png"))
# Factor 1, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_1.png"))
# Factor 2, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_2.png"))
# Factor 3, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_3.png"))
# Factor 4, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_4.png"))
# Factor 5, Presence Absence
knitr::include_graphics(paste0(fp,"/Eps_Pres--Factor_5.png"))